The distribution of the mRNA encoding rat intestinal lactase-phlorizin hydrolase (LPH) was analyzed by ultrastructural in situ hybridization, and compared to the distribution of the cognate protein. Different pictures were obtained depending on the epithelial cell position along the crypt-villus axis: i) cells localized at the crypt base were devoid of LPH mRNA and protein; ii) cells of the crypt-villus junction and of the villus base showed a high level of mRNA but a low amount of enzyme; and iii) enterocytes of the middle and upper part of the villi exhibited an intense protein immunolabeling, but a low content of LPH mRNA. The analysis of the intracellular distribution of the LPH mRNA revealed a gradient of concentration along the cellular axis, as the transcripts were the most abundant in the apical and subapical domains of the enterocytes. In addition, LPH mRNA labeling was often paired or arranged in a circular shape, suggesting that the transcripts may be located in closed vicinity to rounded structures within the cytoplasm. The results indicate that distinct patterns of mRNA and protein occur along the villus height during the continuous process of cell differentiation of the intestinal epithelium. In addition, the emergence of the functional polarity of the enterocytes comes together with the establishment of an intracellular gradient of concentration of the mRNA encoding a brush border enzyme. A link between the intracellular distribution of LPH mRNA molecules and the membranous flow is proposed.